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Detailed information for vg0802410918:

Variant ID: vg0802410918 (JBrowse)Variation Type: SNP
Chromosome: chr08Position: 2410918
Reference Allele: AAlternative Allele: C
Primary Allele: ASecondary Allele: C

Inferred Ancestral Allele : A (evidence from allele frequency in Oryza rufipogon: A: 0.98, C: 0.01, others allele: 0.00, population size: 122. )

Flanking Sequence (100 bp) in Reference Genome:


TGAACCCTTACCATATGCCCTGCATCATGGATGGCAAGCTGTCTGTCATCAGCATGGTGACCCAGCAACAAGTGGATCGATTTCAGTACTCCTTTCGTCC[A/C]
CTAATATAAGGGATTTTTATATTTTAGTTACACTATTTTACCACTCATCTTATTTAAAAAATTATACAAATATAAAAAAATTGTGCTTAAAGTACTTTAA

Reverse complement sequence

TTAAAGTACTTTAAGCACAATTTTTTTATATTTGTATAATTTTTTAAATAAGATGAGTGGTAAAATAGTGTAACTAAAATATAAAAATCCCTTATATTAG[T/G]
GGACGAAAGGAGTACTGAAATCGATCCACTTGTTGCTGGGTCACCATGCTGATGACAGACAGCTTGCCATCCATGATGCAGGGCATATGGTAAGGGTTCA

Allele Frequencies:

Populations Population SizeFrequency of A(primary allele) Frequency of C(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 69.30% 28.60% 2.05% 0.00% NA
All Indica  2759 48.40% 48.10% 3.44% 0.00% NA
All Japonica  1512 99.80% 0.20% 0.00% 0.00% NA
Aus  269 100.00% 0.00% 0.00% 0.00% NA
Indica I  595 31.90% 58.70% 9.41% 0.00% NA
Indica II  465 66.20% 31.40% 2.37% 0.00% NA
Indica III  913 47.90% 51.50% 0.66% 0.00% NA
Indica Intermediate  786 51.00% 46.20% 2.80% 0.00% NA
Temperate Japonica  767 99.90% 0.10% 0.00% 0.00% NA
Tropical Japonica  504 99.80% 0.20% 0.00% 0.00% NA
Japonica Intermediate  241 99.60% 0.40% 0.00% 0.00% NA
VI/Aromatic  96 96.90% 3.10% 0.00% 0.00% NA
Intermediate  90 76.70% 21.10% 2.22% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0802410918 A -> C LOC_Os08g04800.1 downstream_gene_variant ; 3140.0bp to feature; MODIFIER silent_mutation Average:60.925; most accessible tissue: Minghui63 root, score: 84.198 N N N N
vg0802410918 A -> C LOC_Os08g04810.1 downstream_gene_variant ; 1136.0bp to feature; MODIFIER silent_mutation Average:60.925; most accessible tissue: Minghui63 root, score: 84.198 N N N N
vg0802410918 A -> C LOC_Os08g04800-LOC_Os08g04810 intergenic_region ; MODIFIER silent_mutation Average:60.925; most accessible tissue: Minghui63 root, score: 84.198 N N N N

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0802410918 NA 4.78E-06 mr1188 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0802410918 1.29E-06 9.77E-10 mr1739 All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0802410918 NA 1.36E-08 mr1739 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0802410918 NA 7.33E-07 mr1785 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251